each gene set (by comparing the number of significant genes observed on the actual gene list to that observed on each replicate list), to correct these for testing multiple non-independent categories, and to test whether the number of significantly enriched categories is higher than expected (for a fuller description, see Holmans et al. 2009). Unlike methods designed for gene-expression data (where there is typically only one measurement per gene), ALIGATOR uses data from all the SNPs tested in a gene and corrects for the variable numbers of SNPs per gene. Each gene is counted once regardless of how many significant SNPs it contains, thus eliminating the influence of LD between SNPs within genes.
